Extraction of phenotypic traits from taxonomic descriptions for the tree of life using natural language processing
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Endara_et_al-2018-Applications ...
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Final Published Version
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Univ Arizona, Sch Informat, Tucson, AZ 85719 USAIssue Date
2018-03
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BOTANICAL SOC AMER INCCitation
Endara, L., H. Cui, and J. G. Burleigh. 2018. Extraction of phenotypic traits from taxonomic descriptions for the tree of life using natural language processing. Applications in Plant Sciences 6(3): e1035.Journal
APPLICATIONS IN PLANT SCIENCESRights
© 2018 Endara et al. Applications in Plant Sciences is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America. This is an open access article under the terms of the Creative Commons Attribution License.Collection Information
This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at repository@u.library.arizona.edu.Abstract
Premise of the StudyPhenotypic data sets are necessary to elucidate the genealogy of life, but assembling phenotypic data for taxa across the tree of life can be technically challenging and prohibitively time consuming. We describe a semi-automated protocol to facilitate and expedite the assembly of phenotypic character matrices of plants from formal taxonomic descriptions. This pipeline uses new natural language processing (NLP) techniques and a glossary of over 9000 botanical terms. Methods and ResultsOur protocol includes the Explorer of Taxon Concepts (ETC), an online application that assembles taxon-by-character matrices from taxonomic descriptions, and MatrixConverter, a Java application that enables users to evaluate and discretize the characters extracted by ETC. We demonstrate this protocol using descriptions from Araucariaceae. ConclusionsThe NLP pipeline unlocks the phenotypic data found in taxonomic descriptions and makes them usable for evolutionary analyses.Note
Open access journal.ISSN
2168-0450Version
Final published versionSponsors
U.S. National Science Foundation [DEB-1208256, DEB-1541506, DBI-1147266]Additional Links
https://onlinelibrary.wiley.com/doi/full/10.1002/aps3.1035ae974a485f413a2113503eed53cd6c53
10.1002/aps3.1035
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Except where otherwise noted, this item's license is described as © 2018 Endara et al. Applications in Plant Sciences is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America. This is an open access article under the terms of the Creative Commons Attribution License.